I can share with you some insights about deposit transactions showing as an expense and how we can fix this, @noah_thomas-hotm.
This situation happens if these credit card transactions are downloaded directly to the bank account. To fix this, we can exclude them and then re-import or manually enter them using the correct CSV file format.
Here's how to exclude transactions downloaded from your bank:
- Select the Transactions menu.
- Locate the transaction you want to exclude and click this to expand the view.
- Choose the Exclude this transaction checkbox.
- Click Save.

After that, download the last 90 days or more transactions from your bank to get your data back to the feeds. You may refer to this article for detailed steps. It also includes steps on how to categorize and reconcile them after the upload: Add older transactions to QuickBooks Self-Employed.
Keep in touch if you have other concerns with your bank deposits in QuickBooks Self-Employed. I'll be around to help you. Have a nice day ahead.